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coseq

This is the development version of coseq; for the stable release version, see coseq.

Co-Expression Analysis of Sequencing Data


Bioconductor version: Development (3.19)

Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

Author: Andrea Rau [cre, aut] , Cathy Maugis-Rabusseau [ctb], Antoine Godichon-Baggioni [ctb]

Maintainer: Andrea Rau <andrea.rau at inrae.fr>

Citation (from within R, enter citation("coseq")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("coseq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("coseq")
coseq HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.27.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-3
Depends R (>= 4.0.0), SummarizedExperiment, S4Vectors
Imports edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2, scales, HTSFilter, corrplot, HTSCluster, grDevices, graphics, stats, methods, compositions, mvtnorm
System Requirements
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Suggests Biobase, knitr, rmarkdown, testthat, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package coseq_1.27.0.tar.gz
Windows Binary coseq_1.27.0.zip
macOS Binary (x86_64) coseq_1.27.0.tgz
macOS Binary (arm64) coseq_1.27.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/coseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/coseq
Bioc Package Browser https://code.bioconductor.org/browse/coseq/
Package Short Url https://bioconductor.org/packages/coseq/
Package Downloads Report Download Stats